There is only one EMBOSS suite in the tool panel. The EMBOSS tool repo is at 
revision c159a6ded912 and shows version 5.0.0 in the job panel. The tool was 
migrated using galaxy-dist provided migration script and later upgraded using 
the admin panel interface. The job fails with 'command not found error' which 
is resulting from 'Failed to build dependencies'.

Log entries:
{{{
galaxy.tools DEBUG 2013-08-15 15:25:16,021 Building dependency shell command 
for dependency 'emboss'
galaxy.tools.deps WARNING 2013-08-15 15:25:16,022 **** Base Path 
['/share/apps/galaxy/galaxydevelopstaging-tools']
galaxy.tools WARNING 2013-08-15 15:25:16,024 ***** calling 
self.app.toolbox.dependency_manager.find_dep with args emboss 5.0.0 package None

}}}

Line containing asterisk were added by me during debugging.

--
Thanks,
Shantanu


On Aug 15, 2013, at 3:10 PM, Björn Grüning wrote:

> Hi,
> 
>> Thanks for the reply Bjoern. It's installed correctly - green box. The 
>> emboss entries in tool_dependency and tool_shed_repository look fine as 
>> well. 
>> If I directly run an emboss command (e.g. antigenic) from CLI then it seems 
>> to be working.
> 
> can you check a few things or paste the complete warning message from
> Failed to resolve dependency on 'emboss'?
> 
> - Do you have more than one EMBOSS suite installed or showing up in your
> Tool Panel?
> - Which version is shown if you run some EMBOSS tools?
> - I assume tool shed, or test tool shed?
> - can you give us the revision number of EMBOSS that is installed?
> 
> Thanks,
> Bjoern
> 
>> --
>> Shantanu
>> 
>> On Aug 15, 2013, at 2:53 PM, Björn Grüning wrote:
>> 
>>> Hi Shantanu,
>>> 
>>> can you have a look in the Admin menu if EMBOSS is installed correctly
>>> (green) or if it failed (red)?
>>> 
>>> Thanks,
>>> Bjoern
>>> 
>>>> I have migrated Emboss tool from dist to tool-shed using the migration 
>>>> script and later updated it's revision. The tool was installed along with 
>>>> it's dependencies, but it's failing to find them during job run. 
>> It's logging following  'Failed to resolve dependency on 'emboss', ignoring' 
>> warning message in the log file. It seems like 
>> build_dependency_shell_commands method in '/lib/galaxy/tools/__init__.py' is 
>> unable to get installed_tool_dependencies. I am not sure why this would fail 
>> and how to resolve it. I have tried resetting tool metadata several times, 
>> but that didn't help. Appreciate any help on resolving this error. I am 
>> using Galaxy release_2013.06.03 revision.
>>>> 
>>>> Thanks,
>>>> Shantanu
>>>> ___________________________________________________________
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>>> 
>>> 
>>> 
>> 
> 
> 
> 


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